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2022-01-29Automate setting of the development GN3 repoFrederick Muriuki Muriithi
* When developing the GN2 code, there are times we need to use the latest code in GN3, and rather than manually editing the `bin/genenetwork` file every time we need that, this commit enables the use of an environment variable. In this case, launching the application with something like: $ env GN3_DEV_REPO_PATH="$HOME/genenetwork3" ...\ ./bin/genenetwork2 ./the_settings.py -gunicorn-dev will add the path to the development version to the PYTHONPATH. If the GN3_DEV_REPO_PATH variable is not set, then the PYTHONPATH is not altered, and would be as if there is no development version of GN3 in use.
2022-01-29Add "Partial Correlations" UI elements on collections pageFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add UI elements to trigger the partial correlations feature * Connect partial correlation view to the application * Point to correct application element for gunicorn
2022-01-28Update PYTHONPATHzsloan
The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production).
2022-01-28Revert 'bin: Set shebang to sh instead of bash'zsloan
It seems that this also needed to be reverted, because I was getting the error below (which was prevented by reverting to #! /bin/bash): ./bin/genenetwork2: 135: ./bin/genenetwork2: Syntax error: redirection unexpected
2022-01-28Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."Arun Isaac
This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
2022-01-28Revert "bin: Do not set environment variables set by guix shell."Arun Isaac
This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
2022-01-28Revert "README: Document `guix shell' development process."Arun Isaac
This reverts commit e0a260b0de55fbea0c507eb0ca5fbdc3c1a825c0.
2022-01-27Highlight rows selected by filterByIndexzsloan
This adds the "selected" class to rows selected by filterByIndex, which adds highlighting to them I also made the variables in this part of the code camel cased
2022-01-27Changed var to letzsloan
2022-01-27Removed unused variables codezsloan
2022-01-27Added the div for showing the error when the Select Rows text has wrong syntaxzsloan
2022-01-27Replaced the try/catch with something checking for the correct pattern with ↵zsloan
regex, for validating the Select Rows input
2022-01-27Added a comment explaining what the parseIndexString function doeszsloan
2022-01-27Replaced a confusing for loop with something that is (hopefully) easier to ↵zsloan
read and explicitly inverts start_index and end_index when the former is greater than the latter
2022-01-27Changed functions in search_results.js to be camelCased, except for ↵zsloan
change_buttons because it's referenced in many other files
2022-01-27Removed unnecessary variable from for-loop in parse_index_stringzsloan
2022-01-27Changed the placeholder text for the table search to Search Forzsloan
2022-01-27Added some JS disabling form submission on hitting Enter, so that users can ↵zsloan
hit Enter in the Select Rows text area
2022-01-27Moved the Show/Hide Columns text onto the same line as the buttons, to save ↵zsloan
a little vertical space
2022-01-27Changed the glossary question mark to appear at the very end of the colum ↵zsloan
text, in the hopes that this will show up normally for Rob
2022-01-27Changed search result index column to be static (so it doesn't change when ↵zsloan
the user sorts)
2022-01-27Replaced the Select Top feature with one that functions more like the Block ↵zsloan
By Index feature from the trait page; you can now use text indicating index ranges or specific indices, and the filter triggers on either hitting Enter or clicking outside of the text area
2022-01-27Moved the Show/Hide Columns text before the column buttons to save vertical ↵zsloan
space
2022-01-27Reordered search result options as described in Rob's 1/19/2022 e-mailzsloan
2022-01-27Make glossary link question marks italicized and redzsloan
2022-01-27Made the search result table wider for genotype results, since previously ↵zsloan
the Location text was being pushed to a second line (this was actually visible for me as well, not just Rob)
2022-01-27Increased the width of the location columns a bit, since they were being ↵zsloan
pushed onto a second line in some browsers (specifically Robs, but couldn't reproduce in mine, so I just changed it to something that should work for him)
2022-01-27Replaced the info icon in the Peak LOD and Effect Size columns with a ↵zsloan
superscript question mark, since the icon was appearing strangely in some browsers (namely Rob's) but in a while I couldn't reproducd
2022-01-27Fix issue where Geno query was fetching from the chr_num column instead of ↵zsloan
the Chr column (and the chr_num column isn't always populated for certain Genotype datasets)
2022-01-27Increase Y of search result table to 1000px so more rows are visible without ↵zsloan
scrolling
2022-01-27This fixes an issue where you couldn't select more than 150-200 rows when ↵zsloan
submitting search result traits to a collection; it previously just used JQuery and needed to be changed to use DataTables API to select from rows
2022-01-27Fix 'Bad substitution' issueFrederick Muriuki Muriithi
In posix shell, string indexing is undefined. This commit replaces the string indexing with a more portable implementation.
2022-01-26update live jupyter notebooksjgart
Removed bonface's notebook until seaborn gets fixed.
2022-01-26wqflask: Ignore diffs with |ε| < 0.001BonfaceKilz
* wqflask/wqflask/metadata_edits.py (update_phenotype): Filter out values with |ε| < 0.001 when generating the diff file.
2022-01-26user_login: Remove noisy debug statementBonfaceKilz
2022-01-25guix.scm: Inherit package from genenetwork2, not genenetwork3.Arun Isaac
The package definition was likely copied from the genenetwork3 repo resulting in this error. * guix.scm: Inherit package from genenetwork2, not genenetwork3.
2022-01-17update saunak's live jupyter notebookjgart
2022-01-17update live jupyter notebooksjgart
2022-01-11Removed the deferRender setting, since it appears to revent DataTables API ↵zsloan
from being able to access all rows (which caused functions like Select All to only select the first 100-200 rows)
2022-01-06README: Document `guix shell' development process.Arun Isaac
* README.md: Clean up and document `guix shell' development process.
2022-01-06guix.scm: Add guix.scm.Arun Isaac
* guix.scm: New file.
2022-01-06README: Fix typo.Arun Isaac
* README.md: Change clinians to clinicians.
2022-01-06bin: Stop execution on error.Arun Isaac
* bin/genenetwork2: Pass -e flag to sh.
2022-01-06bin: Set shebang to sh instead of bash.Arun Isaac
/bin/sh is present on Guix System and other distros while /bin/bash is present only on other distros. * bin/genenetwork2: Set shebang to sh instead of bash.
2022-01-06bin: Do not set environment variables set by guix shell.Arun Isaac
The Guix python package accepts GUIX_PYTHONPATH instead of PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS when necessary. There is no need to set these environment variables explicitly. * bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS. * README.md [Development]: Remove paragraph on injecting python modules locally.
2022-01-06bin: Set GN2_PROFILE from GUIX_ENVIRONMENT.Arun Isaac
`guix shell' sets the profile path in an environment variable---GUIX_ENVIRONMENT. There is no need to pass it explicity as an input in GN2_PROFILE. * README.md: Remove all references to GN2_PROFILE. * bin/genenetwork2: Set GN2_PROFILE from GUIX_ENVIRONMENT. Do not check the value of GN2_PROFILE now that it is set automatically. Remove all references to GN2_PROFILE in example invocations.
2022-01-05metadata_edits.py: Remove duplicate importsBonfaceKilz
2022-01-05Display correct message on the # of editsBonfaceKilz
2022-01-05Insert data to db by checking the tracked deletions, mods, or addsBonfaceKilz
Prior to this, we only checked for the json files with contained the modifications. However, in the case of double deletions, and double inserts, the data would have been stored in the db anyway; which is a false representation of changes.
2022-01-05Check for any double-inserts or double-deletionsBonfaceKilz
Track any double-inserts or double-deletions
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-27 15:43:58 +0000